EP3378001B8 - Methods for detecting copy-number variations in next-generation sequencing - Google Patents

Methods for detecting copy-number variations in next-generation sequencing Download PDF

Info

Publication number: EP3378001B8
Authority: EP; European Patent Office
Prior art keywords: methods; generation sequencing; number variations; detecting copy; copy
Prior art date: 2015-11-18
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.): Active

Application number

EP16798478.0A

Other languages

German (de)

French (fr)

Other versions

EP3378001A1 (en

EP3378001C0 (en

EP3378001B1 (en

Inventor

Dmitri Ivanov

Zhenyu Xu

Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)

Sophia Genetics SA

Original Assignee

Sophia Genetics SA

Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)

2015-11-18

Filing date

2016-11-18

Publication date

2024-09-04

2016-11-18 Application filed by Sophia Genetics SA filed Critical Sophia Genetics SA

2018-09-26 Publication of EP3378001A1 publication Critical patent/EP3378001A1/en

2024-07-24 Application granted granted Critical

2024-07-24 Publication of EP3378001C0 publication Critical patent/EP3378001C0/en

2024-07-24 Publication of EP3378001B1 publication Critical patent/EP3378001B1/en

2024-09-04 Publication of EP3378001B8 publication Critical patent/EP3378001B8/en

Status Active legal-status Critical Current

2036-11-18 Anticipated expiration legal-status Critical

Classifications

- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
- C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/10—Ploidy or copy number detection
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
- G16B30/10—Sequence alignment; Homology search
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

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Life Sciences & Earth Sciences (AREA)
Physics & Mathematics (AREA)
Health & Medical Sciences (AREA)
Engineering & Computer Science (AREA)
Bioinformatics & Cheminformatics (AREA)
Chemical & Material Sciences (AREA)
Proteomics, Peptides & Aminoacids (AREA)
Analytical Chemistry (AREA)
General Health & Medical Sciences (AREA)
Biophysics (AREA)
Biotechnology (AREA)
Spectroscopy & Molecular Physics (AREA)
Medical Informatics (AREA)
Bioinformatics & Computational Biology (AREA)
Theoretical Computer Science (AREA)
Evolutionary Biology (AREA)
Genetics & Genomics (AREA)
Molecular Biology (AREA)
Organic Chemistry (AREA)
Wood Science & Technology (AREA)
Pathology (AREA)
Immunology (AREA)
Zoology (AREA)
Oncology (AREA)
Microbiology (AREA)
Hospice & Palliative Care (AREA)
Biochemistry (AREA)
General Engineering & Computer Science (AREA)
Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

EP16798478.0A 2015-11-18 2016-11-18 Methods for detecting copy-number variations in next-generation sequencing Active EP3378001B8 (en)

Applications Claiming Priority (2)

Application Number	Priority Date	Filing Date	Title
US201562256748P	2015-11-18	2015-11-18
PCT/EP2016/078113 WO2017085243A1 (en)	2015-11-18	2016-11-18	Methods for detecting copy-number variations in next-generation sequencing

Publications (4)

Publication Number	Publication Date
EP3378001A1 EP3378001A1 (en)	2018-09-26
EP3378001C0 EP3378001C0 (en)	2024-07-24
EP3378001B1 EP3378001B1 (en)	2024-07-24
EP3378001B8 true EP3378001B8 (en)	2024-09-04

Family

ID=58717408

Family Applications (1)

Application Number	Title	Priority Date	Filing Date
EP16798478.0A Active EP3378001B8 (en)	2015-11-18	2016-11-18	Methods for detecting copy-number variations in next-generation sequencing

Country Status (7)

Country	Link
US (3)	US20180330046A1 (en)
EP (1)	EP3378001B8 (en)
CN (1)	CN108292327A (en)
AU (1)	AU2016355983B2 (en)
CA (1)	CA3005791A1 (en)
IL (1)	IL258999B (en)
WO (1)	WO2017085243A1 (en)

Families Citing this family (13)

* Cited by examiner, † Cited by third party
Publication number	Priority date	Publication date	Assignee	Title
WO2018144449A1 (en) *	2017-01-31	2018-08-09	Counsyl, Inc.	Systems and methods for identifying and quantifying gene copy number variations
CN109767810B (en) *	2019-01-10	2021-04-27	上海思路迪生物医学科技有限公司	High-throughput sequencing data analysis method and device
CN111755066B (en) *	2019-03-27	2022-10-18	欧蒙医学诊断（中国）有限公司	Method for detecting copy number variation and equipment for implementing method
US20210027859A1 (en) *	2019-07-22	2021-01-28	Mission Bio, Inc.	Method, Apparatus and System to Detect Indels and Tandem Duplications Using Single Cell DNA Sequencing
GB2587238A (en) *	2019-09-20	2021-03-24	Congenica Ltd	Kit and method of using kit
CN111304299B (en) *	2019-12-11	2022-04-26	北京泛生子基因科技有限公司	Primer combination, kit and method for detecting copy number variation of autosome
CN111242496B (en) *	2020-01-17	2024-11-15	中国平安人寿保险股份有限公司	Method, device, terminal equipment and storage medium for cross-region location testing
CN113496761B (en) *	2020-04-03	2023-09-19	深圳华大生命科学研究院	Methods, devices and applications for determining CNV in nucleic acid samples
CN111508559B (en) *	2020-04-21	2021-08-13	北京橡鑫生物科技有限公司	Method and device for detecting CNV in target area
KR102273257B1 (en)	2020-11-16	2021-07-06	주식회사 엔젠바이오	Copy number variations detecting method based on read-depth and analysis apparatus
CN114774523A (en) *	2021-01-22	2022-07-22	上海羿鸣生物科技有限公司	Method and kit for improving linear amplification detection accuracy through multiple detection and application
CN114745148B (en) *	2022-01-06	2023-02-07	华东师范大学	Method and system for vehicle network CAN bus intrusion detection based on dynamic programming
WO2025141506A1 (en) *	2023-12-27	2025-07-03	Sophia Genetics S.A.	Allele-specific copy number detection from low coverage genotyping data

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number	Priority date	Publication date	Assignee	Title
US9323888B2 (en) *	2010-01-19	2016-04-26	Verinata Health, Inc.	Detecting and classifying copy number variation
RU2014144349A (en) *	2012-04-05	2016-05-27	БГИ Диагносис Ко., Лтд.	METHOD AND SYSTEM OF DETECTION OF VARIATION OF THE NUMBER OF COPIES
EP2738263A1 (en)	2012-11-30	2014-06-04	Fundacion para la Investigacion del Hospital Clinico de la Comunidad Valenciana	Methods for DNA rearrengements analysis
EP2971139A4 (en)	2013-03-15	2016-12-07	Abbott Molecular Inc	Systems and methods for detection of genomic copy number changes
WO2015112619A1 (en)	2014-01-22	2015-07-30	Adam Platt	Methods and systems for detecting genetic mutations

2016
- 2016-11-18 EP EP16798478.0A patent/EP3378001B8/en active Active
- 2016-11-18 US US15/777,091 patent/US20180330046A1/en active Pending
- 2016-11-18 CA CA3005791A patent/CA3005791A1/en active Pending
- 2016-11-18 CN CN201680067423.2A patent/CN108292327A/en active Pending
- 2016-11-18 AU AU2016355983A patent/AU2016355983B2/en active Active
- 2016-11-18 WO PCT/EP2016/078113 patent/WO2017085243A1/en not_active Ceased
2018
- 2018-04-27 IL IL258999A patent/IL258999B/en active IP Right Grant
2021
- 2021-10-20 US US17/505,943 patent/US20220130488A1/en active Pending
- 2021-10-20 US US17/505,934 patent/US20220101944A1/en active Pending

Also Published As

Publication number	Publication date
US20220130488A1 (en)	2022-04-28
US20220101944A1 (en)	2022-03-31
CA3005791A1 (en)	2017-05-26
AU2016355983B2 (en)	2021-12-23
EP3378001A1 (en)	2018-09-26
US20180330046A1 (en)	2018-11-15
BR112018010168A2 (en)	2018-11-21
BR112018010168A8 (en)	2019-02-26
WO2017085243A1 (en)	2017-05-26
CN108292327A (en)	2018-07-17
IL258999B (en)	2020-08-31
EP3378001C0 (en)	2024-07-24
AU2016355983A1 (en)	2018-06-07
EP3378001B1 (en)	2024-07-24
IL258999A (en)	2018-07-31

Publication	Publication Date	Title
EP3378001B8 (en)	2024-09-04	Methods for detecting copy-number variations in next-generation sequencing
DK3604544T3 (en)	2022-02-14	Improved methods for processing dna substrates
EP3228515A4 (en)	2017-11-15	Road condition determination method
EP3126529A4 (en)	2018-04-25	Detecting colorectal neoplasm
EP3180834A4 (en)	2018-04-25	Method for determining cross connection in wireless charging
EP3218522A4 (en)	2018-06-13	Detection methods based on sequencing
GB201412977D0 (en)	2014-09-03	Single nucleotide detection method
EP3163312A4 (en)	2017-07-26	Current sensor
EP3123171A4 (en)	2018-01-03	Protein biomarker profiles for detecting colorectal tumors
GB201608000D0 (en)	2016-06-22	Chromosome detection
EP3152332A4 (en)	2018-01-10	Method for methylation analysis
EP3129915A4 (en)	2018-03-07	Object detection using directional filtering
GB201513128D0 (en)	2015-09-09	Nucleic acid detection method
EP3137629A4 (en)	2017-12-27	Compositions and methods for detecting huanglongbing
EP3106884A4 (en)	2017-09-13	Current sensor
GB201717445D0 (en)	2017-12-06	Method for determining nucleotide sequence
EP3213832A4 (en)	2018-07-18	Spin-molding method
EP3381911A4 (en)	2019-06-26	Method for producing -valerolactone
EP3345996A4 (en)	2019-03-06	Method for producing -glutamyl-valyl-glycine
EP3156484A4 (en)	2017-12-27	Method for judging protein interaction
GB201419113D0 (en)	2014-12-10	Method for determining diffusion
EP3277844A4 (en)	2018-11-07	Methods and materials for detecting rna sequences
EP3230477A4 (en)	2018-07-04	Methods for capturing nucleic acids
EP3128327A4 (en)	2017-08-23	Method for detecting smn protein expression
EP3109630A4 (en)	2017-09-06	Protein detection method using mass spectrometry

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